This code is about codon optimization using quantum-classical hybrid protocols, detailed in Y. K. Chung, et al. "Quantum-classical hybrid approach for codon optimization and its practical applications." bioRxiv (2024): 2024-06.

Contribution: Dongkeun Lee, Jaehee Kim, Junho Lee

Description

• codon_optimization.py : Main code involving 1. Constructing the objective function and constraints 2. Solving the constrained quadratic model 3. Conversion between DNA (or RNA) seqence and qubit vector

• codon_opt.ipynb & codon_LeaphybridCQMsolver.ipynb : Describing functions and classes in codon_optimization.py

• codon_hamiltonian_graph.ipynb : Drawing graphs of the obejctive function for each amino acid sequence, SARS-Cov2 and insulin.

• run_codon_optimization.ipynb : Running codon_optimization.py to solve codon optimization problems using D-Wave LeapCQMHybridSolver

• results_codon_optimization.ipynb : Simulation results from codon_optimization.py

• codon_table: Datasets about Codon Usage Table and Codon Pair Usage Table obtained from COCOPUTs [Link]